HEADER DE NOVO PROTEIN 03-MAR-23 8GD8 TITLE POROUS FRAMEWORK FORMED BY ASSEMBLY OF A BIPYRIDYL-CONJUGATED HELICAL TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIPYRIDYL-CONJUGATED HELICAL PEPTIDE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.S.HESS,A.I.NGUYEN REVDAT 2 25-SEP-24 8GD8 1 COMPND REMARK DBREF SEQRES REVDAT 2 2 1 HET HETNAM FORMUL HELIX REVDAT 2 3 1 LINK ATOM REVDAT 1 15-NOV-23 8GD8 0 JRNL AUTH S.S.HESS,F.COPPOLA,V.T.DANG,P.N.TRAN,P.J.MICKEL,J.OKTAWIEC, JRNL AUTH 2 Z.REN,P.KRAL,A.I.NGUYEN JRNL TITL NONCOVALENT PEPTIDE ASSEMBLY ENABLES CRYSTALLINE, JRNL TITL 2 PERMUTABLE, AND REACTIVE THIOL FRAMEWORKS. JRNL REF J.AM.CHEM.SOC. V. 145 19588 2023 JRNL REFN ESSN 1520-5126 JRNL PMID 37639365 JRNL DOI 10.1021/JACS.3C03645 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.V.AFONINE REMARK 1 TITL TOWARDS AUTOMATED CRYSTALLOGRAPHIC STRUCTURE REFINEMENT WITH REMARK 1 TITL 2 PHENIX.REFINE. REMARK 1 REF ACTA CRYSTALLOGR., SECT. D: V. 68 352 2012 REMARK 1 REF 2 BIOL. CRYSTALLOGR. REMARK 1 REFN ISSN 0907-4449 REMARK 2 REMARK 2 RESOLUTION. 1.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.040 REMARK 3 COMPLETENESS FOR RANGE (%) : 79.7 REMARK 3 NUMBER OF REFLECTIONS : 22123 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.460 REMARK 3 FREE R VALUE TEST SET COUNT : 2093 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 16.5900 - 2.5600 0.95 1603 185 0.1905 0.2093 REMARK 3 2 2.5600 - 2.0300 0.75 1252 123 0.1999 0.1896 REMARK 3 3 2.0300 - 1.7800 0.82 1363 142 0.1959 0.2553 REMARK 3 4 1.7800 - 1.6200 0.84 1431 162 0.2198 0.2188 REMARK 3 5 1.6200 - 1.5000 0.83 1327 142 0.2082 0.1862 REMARK 3 6 1.5000 - 1.4100 0.83 1450 158 0.2216 0.3160 REMARK 3 7 1.4100 - 1.3400 0.84 1416 124 0.2163 0.2616 REMARK 3 8 1.3400 - 1.2800 0.82 1350 138 0.2230 0.2629 REMARK 3 9 1.2800 - 1.2300 0.70 1202 122 0.2094 0.2693 REMARK 3 10 1.2300 - 1.1900 0.72 1236 122 0.2186 0.2917 REMARK 3 11 1.1900 - 1.1500 0.73 1188 128 0.2078 0.2889 REMARK 3 12 1.1500 - 1.1200 0.76 1278 147 0.2060 0.1976 REMARK 3 13 1.1200 - 1.0900 0.78 1250 145 0.2176 0.1833 REMARK 3 14 1.0900 - 1.0600 0.78 1411 129 0.2006 0.2828 REMARK 3 15 1.0600 - 1.0400 0.78 1273 126 0.2303 0.2493 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.105 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.798 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 5.04 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 384 REMARK 3 ANGLE : 1.659 536 REMARK 3 CHIRALITY : 0.077 40 REMARK 3 PLANARITY : 0.011 64 REMARK 3 DIHEDRAL : 32.826 68 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8GD8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1000272637. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-APR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.619920 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22123 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.040 REMARK 200 RESOLUTION RANGE LOW (A) : 16.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.8 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.04922 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.08 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.06539 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: WATER/ACETONITRILE, SLOW COOLING, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 DBREF 8GD8 A 1 11 PDB 8GD8 8GD8 1 11 DBREF 8GD8 B 1 11 PDB 8GD8 8GD8 1 11 DBREF 8GD8 C 1 11 PDB 8GD8 8GD8 1 11 DBREF 8GD8 D 1 11 PDB 8GD8 8GD8 1 11 SEQRES 1 A 11 NIO LEU AIB ALA CYS LEU AIB GLN AIB LEU I77 SEQRES 1 B 11 NIO LEU AIB ALA CYS LEU AIB GLN AIB LEU I77 SEQRES 1 C 11 NIO LEU AIB ALA CYS LEU AIB GLN AIB LEU I77 SEQRES 1 D 11 NIO LEU AIB ALA CYS LEU AIB GLN AIB LEU I77 HET NIO A 1 12 HET AIB A 3 13 HET AIB A 7 12 HET AIB A 9 13 HET I77 A 11 29 HET NIO B 1 12 HET AIB B 3 13 HET AIB B 7 12 HET AIB B 9 13 HET I77 B 11 29 HET NIO C 1 12 HET AIB C 3 13 HET AIB C 7 12 HET AIB C 9 13 HET I77 C 11 29 HET NIO D 1 12 HET AIB D 3 13 HET AIB D 7 12 HET AIB D 9 13 HET I77 D 11 29 HETNAM NIO NICOTINIC ACID HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM I77 5'-(HYDRAZINECARBONYL)[2,2'-BIPYRIDINE]-5-CARBOXAMIDE FORMUL 1 NIO 4(C6 H5 N O2) FORMUL 1 AIB 12(C4 H9 N O2) FORMUL 1 I77 4(C12 H11 N5 O2) FORMUL 5 HOH *10(H2 O) HELIX 1 AA1 AIB A 3 LEU A 10 1 8 HELIX 2 AA2 AIB B 3 LEU B 10 1 8 HELIX 3 AA3 AIB C 3 LEU C 10 1 8 HELIX 4 AA4 AIB D 3 LEU D 10 1 8 LINK C6 NIO A 1 N LEU A 2 1555 1555 1.42 LINK C LEU A 2 N AIB A 3 1555 1555 1.32 LINK C AIB A 3 N ALA A 4 1555 1555 1.33 LINK C LEU A 6 N AIB A 7 1555 1555 1.33 LINK C AIB A 7 N GLN A 8 1555 1555 1.33 LINK C GLN A 8 N AIB A 9 1555 1555 1.32 LINK C AIB A 9 N LEU A 10 1555 1555 1.34 LINK C LEU A 10 N15 I77 A 11 1555 1555 1.43 LINK C6 NIO B 1 N LEU B 2 1555 1555 1.42 LINK C LEU B 2 N AIB B 3 1555 1555 1.33 LINK C AIB B 3 N ALA B 4 1555 1555 1.33 LINK C LEU B 6 N AIB B 7 1555 1555 1.33 LINK C AIB B 7 N GLN B 8 1555 1555 1.33 LINK C GLN B 8 N AIB B 9 1555 1555 1.34 LINK C AIB B 9 N LEU B 10 1555 1555 1.34 LINK C LEU B 10 N15 I77 B 11 1555 1555 1.43 LINK C6 NIO C 1 N LEU C 2 1555 1555 1.42 LINK C LEU C 2 N AIB C 3 1555 1555 1.33 LINK C AIB C 3 N ALA C 4 1555 1555 1.33 LINK C LEU C 6 N AIB C 7 1555 1555 1.33 LINK C AIB C 7 N GLN C 8 1555 1555 1.33 LINK C GLN C 8 N AIB C 9 1555 1555 1.33 LINK C AIB C 9 N LEU C 10 1555 1555 1.34 LINK C LEU C 10 N15 I77 C 11 1555 1555 1.43 LINK C6 NIO D 1 N LEU D 2 1555 1555 1.42 LINK C LEU D 2 N AIB D 3 1555 1555 1.33 LINK C AIB D 3 N ALA D 4 1555 1555 1.33 LINK C LEU D 6 N AIB D 7 1555 1555 1.33 LINK C AIB D 7 N GLN D 8 1555 1555 1.33 LINK C GLN D 8 N AIB D 9 1555 1555 1.33 LINK C AIB D 9 N LEU D 10 1555 1555 1.34 LINK C LEU D 10 N15 I77 D 11 1555 1555 1.43 CRYST1 8.791 16.592 51.150 89.99 89.97 90.01 P 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.113753 0.000022 -0.000060 0.00000 SCALE2 0.000000 0.060270 -0.000011 0.00000 SCALE3 0.000000 0.000000 0.019550 0.00000 HETATM 1 N NIO A 1 1.600 -2.562 22.103 1.00 6.81 N ANISOU 1 N NIO A 1 1145 333 1110 74 16 -178 N HETATM 2 C1 NIO A 1 1.272 -1.691 21.128 1.00 5.49 C ANISOU 2 C1 NIO A 1 653 351 1082 -162 -99 73 C HETATM 3 C2 NIO A 1 0.330 -0.681 21.288 1.00 4.74 C ANISOU 3 C2 NIO A 1 566 274 962 -5 -126 -113 C HETATM 4 C3 NIO A 1 -0.277 -0.556 22.530 1.00 5.67 C ANISOU 4 C3 NIO A 1 573 504 1079 189 29 -129 C HETATM 5 C4 NIO A 1 0.042 -1.442 23.536 1.00 6.56 C ANISOU 5 C4 NIO A 1 861 556 1074 187 -71 -292 C HETATM 6 C5 NIO A 1 0.980 -2.420 23.279 1.00 7.08 C ANISOU 6 C5 NIO A 1 1115 477 1100 -111 -5 -232 C HETATM 7 C6 NIO A 1 0.000 0.284 20.210 1.00 4.78 C ANISOU 7 C6 NIO A 1 440 304 1073 62 -157 -70 C HETATM 8 O1 NIO A 1 0.053 1.492 20.387 1.00 5.54 O ANISOU 8 O1 NIO A 1 647 322 1136 52 127 134 O HETATM 9 H1 NIO A 1 1.698 -1.770 20.305 1.00 6.66 H HETATM 10 H3 NIO A 1 -0.895 0.122 22.682 1.00 6.88 H HETATM 11 H4 NIO A 1 -0.367 -1.383 24.369 1.00 7.94 H HETATM 12 H5 NIO A 1 1.194 -3.014 23.963 1.00 8.57 H